The cause of conjunctivitis is established by the isolation of primary pathogens eg, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria gonorrhoeae, Chlamydia trachomatis or Streptococcus pyogenes.

The culture of organisms such as Staphylococcus aureus, Staphylococcus epidermidis, Moraxella spp, Pseudomonas spp or coliforms may reflect non-pathogenic flora but in certain circumstances these organisms can be pathogenic.

Examination of the swab/fluid may allow diagnosis of herpes simplex, varicella zoster, fungal or acanthamoebic keratitis, although culture of corneal scrapings/biopsy will give a higher yield.